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PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants
Daniel Longhi Fernandes Pedro1, Alan Péricles Rodrigues Lorenzetti2, Douglas Silva Domingues1,3
1Department of Computer Science, Bioinformatics Graduation Program (PPGBIOINFO), Federal University of Technology - Paraná, Cornélio Procópio, PR, Brazil.
Database : the Journal of Biological Databases and Curation
|August 14, 2018
Summary
PlaNC-TE is a new database organizing plant non-coding RNA and transposable element data. It reveals 14,350 overlaps, aiding genome annotation and understanding TE-ncRNA interactions.
Area of Science:
- Genomics
- Bioinformatics
- Plant Science
Background:
- Transposable elements (TEs) significantly contribute to genetic variation in eukaryotes, especially plants, where they can constitute up to 90% of the genome.
- Non-coding RNAs (ncRNAs) are crucial regulators of gene expression.
- Understanding the interplay between ncRNAs and TEs is vital but data organization remains challenging.
Purpose of the Study:
- To develop PlaNC-TE, a user-friendly portal for integrated plant ncRNA-TE data.
- To provide a comprehensive knowledgebase for analyzing ncRNA-TE interactions in plants.
- To facilitate genome annotation and the study of TE-ncRNA functional mechanisms.
Main Methods:
- Integration and analysis of ncRNA and TE data from 40 sequenced plant genomes.
- Development of the PlaNC-TE web portal (http://planc-te.cp.utfpr.edu.br) for data access.
- Identification and cataloging of overlaps between ncRNAs and TEs.
Main Results:
- A total of 14,350 overlaps between ncRNAs and TEs were identified across 40 plant genomes.
- The PlaNC-TE database offers browsing, searching, and downloading capabilities for all analyzed ncRNA and TE data.
- This represents the first database resource for extensive investigation of TE-ncRNA functions in plants.
Conclusions:
- PlaNC-TE successfully organizes complex plant ncRNA-TE data, offering novel insights.
- The database aids in improving plant genome annotation strategies.
- PlaNC-TE serves as a unique resource for exploring the functional relationships between transposable elements and non-coding RNAs in plants.
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